Abstract
Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine and leucine) and N,N-dimethylformamide (DMF) in gas phase have been carried out using density functional theory (DFT) and ab initio calculations at the B3LYP/6-311++G** and MP2/6-311++G** theory levels. The structures, binding energy, stretching frequency and bond characteristics of the mentioned complexes were calculated. The NH2 and COOH groups of amino acids form different types of hydrogen bonds with the DMF molecule, as well as alkyl side chains. High binding energy suggests multiple hydrogen bonds present in one complex. The nearly linear OH⋅⋅⋅O and NH⋅⋅⋅O contacts are stronger than a conventional hydrogen bond interaction with their H⋅⋅⋅O separation between 1.74 and 2.14 Å. The weaker CH⋅⋅⋅O H-bond is also discussed as being a crucial interaction in biological systems involving amino acids. The formation of this interaction results in a blue shift in the CH stretching frequency.
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Adcock, J.L., Zhang, H.: Polarized C-H groups as novel hydrogen-bond donors in hydryl-F-alkyl esters: unequivocal examples for the “Pinchas Effect”. J. Org. Chem. 60, 1999–2002 (1995)
Angelo, V., Jack, D.D.: Lone-pair directionality in hydrogen-bond potential functions for molecular mechanics calculations: the inhibition of human carbonic anhydrase II by sulfonamides. J. Am. Chem. Soc. 107, 7653–7658 (1985)
Bader, R.F.W.: Atom in Molecules: A Quantum Theory, International Series of Monographs in Chemistry. Oxford University Press, Oxford (1990)
Bader, R.F.W.: A bond path: a universal indicator of bonded interactions. J. Phys. Chem. A 102, 7314–7323 (1998)
Biegler-Konig, F., Bader, R.F.: AIM 2000, Version 2 (2002)
Boys, S.F., Bernardi, F.: Calculations of small molecular interactions by differences of separate total energies. Some procedures with reduced errors. Mol. Phys. 19, 553–566 (1970)
Clark, T., Chandrasekhar, J., Spitznagel, G.W., Schleyer, P.V.R.: Efficient diffuse function-augmented basis sets for anion calculations. III: The 3-21+G basis set for first-row elements, Li-F. J. Comp. Chem. 4, 294–301 (1983)
Dan, T.M., Kwangho, N., Gao, J.A.: Transition state stabilization and α-amino carbon acidity in alanine racemase. J. Am. Chem. Soc. 128, 8114–8115 (2006)
Frisch, M.J., Pople, J.A., Binkley, J.S.: Self-consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets. J. Chem. Phys. 80, 3265–3269 (1984)
Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Montgomery, J.A. Jr., Vreven, T., Kudin, K.N., Burant, J.C., Millam, J.M., Iyengar, S.S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G.A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J.E., Hratchian, H.P., Cross, J.B., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Ayala, P.Y., Morokuma, K., Voth, G.A., Salvador, P., Dannenberg, J.J., Zakrzewski, V.G., Dapprich, S., Daniels, A.D., Strain, M.C., Farkas, O., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Ortiz, J.V., Cui, Q., Baboul, A.G., Clifford, S., Cioslowski, J., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, A., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Gonzalez, C., Pople, J.A.: Gaussian03. Gaussian. Inc., Pittsburgh (2003)
Fuqiang, B., Kathryn, N.R., James, W.G., Russell, J.B.: Recent applications of density functional theory calculations to biomolecules. Theor. Chem. Acc. 108, 1–11 (2002)
Hobza, P., Spirko, V., Havlas, Z., Buchhold, K., Reimann, B., Barth, H.D., Brutschy, B.: Anti- hydrogen bond between chloroform and fluorobenzene. Chem. Phys. Lett. 299, 180–186 (1999)
Jordan, R.Q., Steven, C.Z., Janet, E.D.B., Isaiah, S.: Does the A⋅T or G⋅C base-pair possess enhanced stability? Quantifying the effects of CH⋅⋅⋅O interactions and secondary interactions on base-pair stability using a phenomenological analysis and ab initio calculations. J. Am. Chem. Soc. 129, 934–941 (2007)
Loos, P.F., Assfeld, X., Rivail, J.L.: Intramolecular interactions and cis peptidic bonds. Theor. Chem. Acc. 118, 165–171 (2007)
Magalhaes, A.L., Madail, S.R.R.S., Ramos, M.J.: Prediction of the Raman spectrum of the aqueous formate anion by a combined density functional theory and self-consistent-reaction-field study. Theor. Chem. Acc. 105, 68–76 (2000)
Mizuno, K., Ochi, T., Shindo, Y.: Hydrophobic hydration of acetone probed by nuclear magnetic resonance and infrared: Evidence for the interaction C–H⋅⋅⋅OH2. J. Chem. Phys. 109, 9502–9507 (1998)
Parr, R.G., Yang, W.: Density-Functional Theory of Atoms and Molecules. Oxford Science, Oxford (1989)
Perutz, M.F.: The role of aromatic rings as hydrogen-bond acceptors in molecular recognition. Phil. Trans. R. Soc. A 345, 105–112 (1993)
Pinchas, S.: Infrared absorption of aldehydic C-H group. Anal. Chem. 29, 334–339 (1957)
Pinchas, S.: Intramolecular hydrogen bonding in o-nitrobenzaldehyde and related compounds. J. Phys. Chem. 67, 1862–1865 (1963)
Robert, P.A., Maria, B., Sarah, L.P.: The orientation of N–H⋅⋅⋅O=C and N–H⋅⋅⋅N hydrogen bonds in biological systems: how good is a point charge as a model for a hydrogen bonding atom? J. Comput. -Aided Mol. Des. 11, 479–490 (1997)
Satonaka, H., Abe, K., Hirota, M.: NMR spectroscopic study of the conformational preference of methoxycarbonyl and methyl substituted thiophenecarbaldehydes. Possibility of a hydrogen-bond-like interaction between formyl C–H and the ester carbonyl group. Bull. Chem. Soc. Jpn. 61, 2031–2037 (1988)
Sijpkes, A.H., Staneke, P.O., Somsen, G.: Enthalpies of interaction of some N-acetyl amides of L-serine. L-threonine and L-hydroxyproline dissolved in N,N-dimethylformamide at 298.15 K. Thermochim. Acta 167, 65–72 (1990)
Sammes, M.P., Harlow, R.L.: Intramolecular hydrogen bonds involving polar carbon–hydrogen bonds: infrared and 1H nuclear magnetic resonance spectra of some cyanomethyl and benzyl sulphones. J. Chem. Soc. Perkin. Trans. II, 1130–1135 (1976)
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Ren, XH., Wang, HJ. Hydrogen-Bonding Interaction in a Complex of Amino Acid with N,N-Dimethylformamide Studied by DFT Calculations. J Solution Chem 38, 303–313 (2009). https://doi.org/10.1007/s10953-009-9368-5
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DOI: https://doi.org/10.1007/s10953-009-9368-5